Organism : Methanococcus maripaludis S2 | Module List :
MMP0018

LysR family transcriptional regulator

CircVis
Functional Annotations (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0018
(Mouseover regulator name to see its description)

Warning: No Regulators were found for MMP0018!

Warning: MMP0018 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
829 1.00e+03 cagttGCgg.aaggA
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830 1.20e+04 gTtAGgGG
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979 1.70e-05 ggGGGagtt
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980 2.00e+00 ctctTctCa.ATa.ccccGTA
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for MMP0018

MMP0018 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for MMP0018

MMP0018 has total of 50 gene neighbors in modules 85, 166
Gene neighbors (50)
Gene Common Name Description Module membership
Antisense_1 None 85, 104
MMP0018 LysR family transcriptional regulator 85, 166
MMP0097 transcriptional regulator 58, 166
MMP0140 (NiFe) hydrogenase maturation protein HypF 4, 85
MMP0161 comB 2-phosphosulfolactate phosphatase 85, 104
MMP0211 hypothetical protein MMP0211 45, 85
MMP0238 hypothetical protein MMP0238 160, 166
MMP0424 hypothetical protein MMP0424 85, 163
MMP0454 hypothetical protein MMP0454 85, 163
MMP0459 hypothetical protein MMP0459 85, 101
MMP0478 hypothetical protein MMP0478 5, 85
MMP0512 fmdB molybdenum containing formylmethanofuran dehydrogenase subunit B 85, 101
MMP0517 hypothetical protein MMP0517 69, 85
MMP0522 hypothetical protein MMP0522 42, 85, 146, 153
MMP0523 ABC transporter ATP-binding protein 42, 85, 146, 153
MMP0538 hypothetical protein MMP0538 85, 166
MMP0547 RecJ-like protein 22, 166
MMP0558 hypothetical protein MMP0558 50, 166
MMP0565 hypothetical protein MMP0565 42, 85
MMP0652 hypothetical protein MMP0652 131, 166
MMP0731 exodeoxyribonuclease VII small subunit 85, 104
MMP0756 hypothetical protein MMP0756 42, 166
MMP0758 HNH endonuclease:HNH nuclease 45, 166
MMP0759 hypothetical protein MMP0759 45, 166
MMP0789 codB cytosine permease 72, 85
MMP0794 hypothetical protein MMP0794 85, 163
MMP0807 carboxymuconolactone decarboxylase-like protein 42, 85, 155
MMP0813 hypothetical protein MMP0813 146, 166
MMP0828 hypothetical protein MMP0828 45, 85, 163
MMP0835 hypothetical protein MMP0835 85, 146
MMP0842 hypothetical protein MMP0842 69, 166
MMP0864 napA-2 Na+/H+ exchanger 50, 146, 166
MMP0871 hypothetical protein MMP0871 22, 153, 166
MMP0892 GCN5-like N-acetyltransferase 42, 85
MMP1125 hypothetical protein MMP1125 69, 85, 163
MMP1173 zinc/iron permease 45, 85
MMP1179 methyltransferase 85, 110, 151
MMP1180 hypothetical protein MMP1180 45, 85
MMP1268 hypothetical protein MMP1268 85, 166
MMP1291 glycoside hydrolase family protein 43, 166
MMP1292 glycoside hydrolase 15-like protein 43, 166
MMP1294 glgA starch synthase 43, 150, 166
MMP1296 pfkC ADP-specific phosphofructokinase 45, 166
MMP1423 aldehyde dehydrogenase 85, 163
MMP1501 phosphodiesterase 85, 163
MMP1535 hypothetical protein MMP1535 36, 85
MMP1604 hypothetical protein MMP1604 43, 166
MMP1605 pyruvate kinase 1, 54, 146, 166
MMP1653 hypothetical protein MMP1653 150, 166
MMP1654 hypothetical protein MMP1654 50, 166
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for MMP0018
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend